DOTS-Finder: a comprehensive tool for assessing driver genes in cancer genomes

Melloni, Giorgio EM; Ogier, Alessandro GE; de Pretis, Stefano; Mazzarella, Luca; Pelizzola, Mattia; Pelicci, Pier Giuseppe; Riva, Laura

doi:10.1186/gm563

Table 1 Significantly mutated genes identified by DOTS-Finder in four cancer types

From: DOTS-Finder: a comprehensive tool for assessing driver genes in cancer genomes

Acute myeloid leukemia (S = 196, MNSp = 11)			Thyroid carcinoma (S = 326, MNSp = 19)			Breast cancer (S = 1046, MNSp = 36)			Bladder carcinoma (S = 145, MNSp = 177)
Gene name	NS frequency	q-value	Gene name	NS frequency	q-value	Gene name	NS frequency	q-value	Gene name	NS frequency	q-value
TSGs
CEBPA	0.066	0	TG	0.049	8.0E-10	CBFB	0.021	0	ARID1A	0.241	0
NPM1	0.276	0	EMG1	0.018	5.3E-08	CDH1	0.062	0	CDKN1A	0.145	0
RUNX1	0.092	0	RPTN	0.025	9.1E-06	GATA3	0.095	0	KDM6A	0.214	0
TET2	0.087	0	PPM1D	0.015	0.0054	MAP2K4	0.039	0	TP53	0.262	0
TP53	0.077	0	TMCO2	0.009	0.0056	MAP3K1	0.070	0	ELF3	0.076	1.2E-10
WT1	0.061	0	IL32	0.009	0.0152	PTEN	0.040	0	MLL2	0.262	1.2E-10
RAD21	0.026	3.3E-06	*DNMT3A*	0.015	0.2896	TP53	0.338	0	EP300	0.152	3.0E-09
PHF6	0.031	3.4E-06				TBX3	0.022	1.1E-12	RB1	0.110	2.3E-08
STAG2	0.031	1.4E-05				MLL3	0.065	5.9E-12	SPTAN1	0.097	3.0E-06
EZH2	0.015	0.0007				AOAH	0.019	3.9E-10	MLL3	0.200	6.1E-06
ASXL1	0.026	0.0014				CTCF	0.021	7.9E-10	CREBBP	0.131	1.2E-05
HNRNPK	0.010	0.0083				RUNX1	0.024	3.2E-06	STAG2	0.090	7.6E-05
CALR	0.010	0.0142				NCOR1	0.038	3.9E-06	FOXQ1	0.048	0.0060
CBFB	0.010	0.0572				RB1	0.021	6.1E-06	TXNIP	0.055	0.0079
CBX7	0.005	0.0948				NCOR2	0.032	0.0003	FAT1	0.110	0.0370
*BCOR*	0.010	0.1971				STXBP2	0.010	0.0004	FBXW7	0.069	0.0428
						AQP7	0.008	0.0017	GCC2	0.069	0.0800
						ZFP36L1	0.012	0.0046	ZNF513	0.055	0.0911
						RBMX	0.012	0.0056	*KLF5*	0.062	0.1184
						GPS2	0.007	0.0095	*GPS2*	0.028	0.2599
						CASP8	0.015	0.0104	*NHLRC1*	0.021	0.2635
						CDKN1B	0.008	0.0125
						UBC	0.008	0.0155
						MED23	0.013	0.0224
						MYB	0.012	0.0407
						*CCDC144NL*	0.008	0.1268
						*GNRH2*	0.003	0.2062
						*HNF1A*	0.009	0.7280
OGs
CEBPA	0.066	0	BRAF	0.561	0	AKT1	0.022	0	TP53	0.262	0
DNMT3A	0.260	0	HRAS	0.037	0	PIK3CA	0.285	0	NFE2L2	0.076	6.1E-06
FLT3	0.270	0	NRAS	0.080	0	TP53	0.338	0	ERBB3	0.117	1.1E-05
IDH1	0.097	0	TG	0.049	3.5E-08	TBX3	0.022	9.0E-10	RARG	0.069	1.5E-05
IDH2	0.102	0	DNASE2	0.009	0.0694	SF3B1	0.017	3.4E-08	*IRS4*	0.014	0.6550
NRAS	0.077	0	PRDM9	0.018	0.0816	FOXA1	0.017	7.7E-05	*ELP5*	0.014	0.6550
TP53	0.077	0	*DICER1*	0.009	0.1070	HIST1H3B	0.008	0.0001	*RPS6*	0.021	0.6550
U2AF1	0.041	0	*ZNF845*	0.018	0.1070	MEF2A	0.014	0.0002
			*PRG4*	0.012	0.1085	PIK3R1	0.025	0.0008
			*PTTG1IP*	0.012	0.1085	ATN1	0.017	0.0425
						AKD1	0.018	0.0431

MNSp, median number of non-silent mutations per patient; NS freq, non-synonymous mutation frequency among samples; S, number of samples. Genes in bold are the closest to significance in the ranking.

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